FIGURE 2.

Different criteria for pseudoknot removal lead to different results for a pseudoknot in the group I intron structure (PDB ID: 1ZZN) (Stahley and Strobel 2005). Helices P3 and P7 are involved in a pseudoknot. There are two possible solutions to create a nested structure: Keep P3 and break P7 or keep P7 and break P3. In terms of the number of base pairs (BPS), both solutions are equivalent and optimal (both have 6 BPS). In terms of hydrogen bonds (HB), keeping P3 is optimal, because it has 16 hydrogen bonds where P7 has only 15. The image of the structure is made with the S2S software (Jossinet and Westhof 2005).